AW: How to refer to side-chain via tcl-force scripting?

From: Norman Geist (
Date: Fri Jun 13 2014 - 02:56:03 CDT

Guess no! A good way to do it, is do write a TCL script for VMD to prepare
some kind of config file containing the information you need and source this
configuration within your TCLForces script. Like (expects to have a molecule
loaded already):




puts "Input) Molid?"

gets stdin molid

puts "Input) Resids?"

gets stdin resids


array unset sidechains; #save restart

array set sidechains {}

foreach resid $resids {

                set sel [atomselect $molid "resid $resid and sidechain"]

                set sidechains($resid) [$sel get index]

                $sel delete



set fp [open "prepared.conf.tcl" w]

puts $fp [list array set sidechains [array get sidechains]]

close $fp

puts "Info) Done, you're are now prepared!"


So within your TclForces script:


source prepared.conf.tcl

#loop over sidechains

foreach resid [array names sidechains] {

                puts "Now doing something with sidechain of resid $resid
having this atoms: $sidechains($resid)"



Norman Geist.


Von: [] Im Auftrag
von zeynab mohamad hoseyni
Gesendet: Freitag, 13. Juni 2014 07:53
Betreff: namd-l: How to refer to side-chain via tcl-force scripting?


Dear all,


I need to impose force on the side-chain of some residues, using tcl-force
scripting. Do you know if

the tcl-force interface provides any command so that you can refer to
side-chain of the desired residue?


Thanks in advance for your help,


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